1. A poster on our paper
entitled Boosting Protein Threading
Accuracy won theBest Poster Award in RECOMB 2009 held in Tucson, Arizona
(May 17-21, 2009). RECOMB is one of the best conferences in the field of
Computational Biology and Bioinformatics.

2. The
following poster won the Best Poster Award in
CASP8 conference held in Cagliari,
Sardinia, Italy (Dec 3-7, 2008). CASP is the most prestigious
competition in the field of protein structure prediction.

3. My protein structure
prediction program RAPTOR ranked No.2-No.4 among
all automated programs in CASP8, according to several assessments (Grishin, McGuffin, Zhang) and the
CASP8 official ranking.The abstract
about RAPTOR in CASP8 is available at RAPTOR-CASP8.doc.
Please note that RAPTOR in CASP8 is very different from previous RAPTORs and there is only one RAPTOR participating in
CASP8. Here I give a list of people who contributed to RAPTOR in CASP8.

1)Jinbo Xu and his
students JianPeng and Feng Zhao at TTI-Chicago: major contributors

6)XinGao:
RAPTOR web server setup and running RAPTOR in the very early stage of CASP8

7)Ming Li: providing some computing resources

This new version RAPTOR
does not do any fragment assembly at all. We are working on a totally new web
server to provide free protein modeling service. The binary code of some
modules in the new version RAPTOR will also be available for download
gradually.

Jinbo Xu. Rapid Protein Side-Chain Packing via
Tree Decomposition. RECOMB 2005. [ps][pdf] A software package based
on this approach can be downloaded at SCATD. A full version
of this paper appeared at the Journal of the ACM.

Jinbo
Xu and Ming Li. Assessment of RAPTOR's
Linear Programming Approach in CAFASP3, CASP5 (Fifth Critical Assessment of
Structure Prediction) special issue, Proteins: Structure, Function and Genetics. Oct, 2003. (an
invited paper, the only one voted by all the CASP5/CAFASP3 attendees according
to novelty and performance.) [ps][pdf]

Jinbo Xu, Ying Xu, Dongsup
Kim and Ming Li. RAPTOR: Optimal Protein Threading by Linear Programming, the
inaugural issue, Journal of Bioinformatics and Computational Biology, April
2003.[ps] [pdf] A software package RAPTOR has
been developed based on the method proposed in this paper. RAPTOR ranks first
among all non-meta servers in CAFASP3 (Third Critical
Assessment of Fully Automated Structure Prediction). RAPTOR also ranks third
among all non-meta servers in CASP6 according tohttp://www.bioinformatics.buffalo.edu/casp6/.
RAPTOR has been commercialized to BioinformaticsSolutions
Inc., Waterloo, Canada and has been licensed to
some pharmaceutical companies such as Merck.

Invited Talks

Protein threading by nonlinearly combining
evolutionary and non-evolutionary information. The University of Minnesota,
April 2009.